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Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.20 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.64 53.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.966 α = 90 b = 78.659 β = 93.121 c = 107.027 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 41.581 97.3 0.132 0.187 0.132 0.98 3.6 2.1 56390 33.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.26 0.725 1.024 0.723 0.395 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.2 41.581 56389 1135 96.847 0.208 0.207 0.267 0.2857 42.442
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.931 0.099 0.739 -2.666
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.652 r_dihedral_angle_3_deg 13.135 r_lrange_it 10.142 r_lrange_other 10.142 r_dihedral_angle_2_deg 9.389 r_dihedral_angle_1_deg 6.437 r_scangle_it 5.813 r_scangle_other 5.812 r_mcangle_it 4.874 r_mcangle_other 4.874
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 14.652 r_dihedral_angle_3_deg 13.135 r_lrange_it 10.142 r_lrange_other 10.142 r_dihedral_angle_2_deg 9.389 r_dihedral_angle_1_deg 6.437 r_scangle_it 5.813 r_scangle_other 5.812 r_mcangle_it 4.874 r_mcangle_other 4.874 r_scbond_it 3.589 r_scbond_other 3.588 r_mcbond_it 3.061 r_mcbond_other 3.059 r_angle_refined_deg 1.368 r_angle_other_deg 0.732 r_nbd_other 0.243 r_symmetry_nbd_other 0.213 r_nbd_refined 0.209 r_symmetry_nbd_refined 0.202 r_symmetry_xyhbond_nbd_refined 0.192 r_xyhbond_nbd_refined 0.185 r_nbtor_refined 0.175 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.083 r_chiral_restr 0.063 r_bond_refined_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.005 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7704 Nucleic Acid Atoms Solvent Atoms 561 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building